Change sed command to fit Debian 9

genome-nexus · Aug 22, 2024 · c116f77 · c116f77
1 parent c8684e2
commit c116f77
Showing 1 changed file with 1 addition and 7 deletions.
diff --git a/scripts/import_mongo.sh b/scripts/import_mongo.sh
@@ -72,13 +72,7 @@ do
 
     echo "Transforming $mutation_assessor_tsv_file"
     # Rename the columns
-    if [ -f "${DIR}/../data/common_input/${mutation_assessor_tsv_file}" ]; then
-        echo "File exists: ${DIR}/../data/common_input/${mutation_assessor_tsv_file}"
-    else
-        echo "File not found: ${DIR}/../data/common_input/${mutation_assessor_tsv_file}"
-        exit 1
-    fi
-    sed 's/uniprotId\tSV\thgvspShort\tF_score\tF_impact\tMSA\tMAV/uniprotId\tsv\thgvspShort\tf_score\tf_impact\tmsa\tmav/' ${DIR}/../data/common_input/$mutation_assessor_tsv_file
+    sed -i 's/uniprotId\tSV\thgvspShort\tF_score\tF_impact\tMSA\tMAV/uniprotId\tsv\thgvspShort\tf_score\tf_impact\tmsa\tmav/' ${DIR}/../data/common_input/$mutation_assessor_tsv_file
     # Add a new column "_id" (uniprotId,hgvspShort)
     awk -F'\t' 'BEGIN{OFS="\t"} NR==1{print "_id",$0; next} {print $1","$3,$0}' ${DIR}/$mutation_assessor_tsv_file > ${DIR}/../data/common_input/processed_$mutation_assessor_tsv_file